Genetic Variant NM_001443.3:c.334-135C>T (chr2-88123239-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001443.3(FABP1):c.334-135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 709,064 control chromosomes in the GnomAD database, including 19,880 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 3041 hom., cov: 33)

Exomes 𝑓: 0.22 ( 16839 hom. )

Consequence

FABP1
NM_001443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12

Publications

16 publications found

Variant links:

Genes affected

FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

FABP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP1	NM_001443.3 link	c.334-135C>T		intron_variant	Intron 3 of 3	ENST00000295834.8	NP_001434.1	P07148Q6FGL7Q05CP7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FABP1	ENST00000295834.8 link	c.334-135C>T	intron_variant	Intron 3 of 3	1	NM_001443.3	ENSP00000295834.3	P07148
FABP1	ENST00000495375.1 link	n.1874C>T	non_coding_transcript_exon_variant	Exon 4 of 4	3
FABP1	ENST00000393750.3 link	c.*1213C>T	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000377351.3	A8MW49

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26588

AN:

152048

Hom.:

3036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0981

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.531

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.218

AC:

121682

AN:

556898

Hom.:

16839

Cov.:

AF XY:

0.228

AC XY:

66600

AN XY:

292082

show subpopulations

African (AFR)

AF:

0.0869

AC:

1177

AN:

13538

American (AMR)

AF:

0.124

AC:

2309

AN:

18636

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

2281

AN:

14560

East Asian (EAS)

AF:

0.508

AC:

15688

AN:

30872

South Asian (SAS)

AF:

0.443

AC:

19799

AN:

44724

European-Finnish (FIN)

AF:

0.122

AC:

5549

AN:

45610

Middle Eastern (MID)

AF:

0.197

AC:

438

AN:

2224

European-Non Finnish (NFE)

AF:

0.191

AC:

68514

AN:

357944

Other (OTH)

AF:

0.206

AC:

5927

AN:

28790

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4235

8470

12704

16939

21174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1096

2192

3288

4384

5480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.175

AC:

26594

AN:

152166

Hom.:

3041

Cov.:

AF XY:

0.179

AC XY:

13320

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0978

AC:

4061

AN:

41504

American (AMR)

AF:

0.130

AC:

1984

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

581

AN:

3468

East Asian (EAS)

AF:

0.531

AC:

2749

AN:

5178

South Asian (SAS)

AF:

0.468

AC:

2255

AN:

4814

European-Finnish (FIN)

AF:

0.106

AC:

1120

AN:

10586

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13270

AN:

68004

Other (OTH)

AF:

0.177

AC:

375

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1092

2184

3276

4368

5460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.202

Hom.:

1810

Bravo

AF:

0.166

Asia WGS

AF:

0.453

AC:

1572

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.47

(source)

DANN

Benign

0.44

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over